This is a document that summarized the PCA analysis performed on the RSP simulated clouds LUT. (R routine to perform this analysis:runpcaana)
read LUT and print some variable examples
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## [1] "processing NN_clouds_20150701.nc"
## [1] "file ~/R/oracles_polar_algorithm//data/NN_clouds_20150701.nc has 3 dimensions:"
## [1] "index Size: 1349"
## [1] "waveln Size: 7"
## [1] "viewzenith Size: 640"
## [1] "------------------------"
## [1] "file ~/R/oracles_polar_algorithm//data/NN_clouds_20150701.nc has 8 variables:"
## [1] "float sizea[index] Longname:A size parameter (effective radius) Missval:1e+30"
## [1] "float sizeb[index] Longname:B size parameter (effective variance) Missval:1e+30"
## [1] "float cldtop[index] Longname:Cloud top height Missval:1e+30"
## [1] "float cod[index] Longname:Cloud optical depth Missval:1e+30"
## [1] "float sza[index] Longname:Solar zenith angle Missval:1e+30"
## [1] "float azi[index] Longname:Solar azimuth angle (from due north) Missval:1e+30"
## [1] "float ref_i[index,waveln,viewzenith] Longname:Reflectance, (Stokes vector I) Missval:1e+30"
## [1] "float ref_q[index,waveln,viewzenith] Longname:Q Reflectance, (Stokes vector Q) Missval:1e+30"
## [1] " file variable names:"
## [1] "sizea" "sizeb" "cldtop" "cod" "sza" "azi" "ref_i" "ref_q"
## [1] " file variable names:"
## [1] "sizea" "sizeb" "cldtop" "cod" "sza" "azi" "ref_i" "ref_q"
## [1] "variable sizea dim:"
## [1] 1349
## [1] "variable sizea sample data:"
## [1] 7.5 7.5 7.5 7.5 7.5 7.5
## [1] "variable sizeb dim:"
## [1] 1349
## [1] "variable sizeb sample data:"
## [1] 0.05 0.05 0.05 0.05 0.05 0.05
## [1] "variable cldtop dim:"
## [1] 1349
## [1] "variable cldtop sample data:"
## [1] 1000 1000 1000 1000 1000 1000
## [1] "variable cod dim:"
## [1] 1349
## [1] "variable cod sample data:"
## [1] 1 1 1 1 1 1
## [1] "variable sza dim:"
## [1] 1349
## [1] "variable sza sample data:"
## [1] 10.00001 10.00001 10.00001 10.00001 10.00001 10.00001
## [1] "variable azi dim:"
## [1] 1349
## [1] "variable azi sample data:"
## [1] 0 2 5 10 20 30
## [1] "variable ref_i dim:"
## [1] 1349 7 640
## [1] "variable ref_i sample data:"
## [1] 0.2634877 0.2634730 0.2633957 0.2631150 0.2619549 0.2601073
## [1] "variable ref_q dim:"
## [1] 1349 7 640
## [1] "variable ref_q sample data:"
## [1] -0.1171747 -0.1171856 -0.1172425 -0.1174415 -0.1181891 -0.1193412
## [1] "variable sizea dim:"
## [1] 1349
## [1] "variable sizea sample data:"
## [1] 7.5 7.5 7.5 7.5 7.5 7.5
## [1] "processing single col array"
## [1] "variable sizeb dim:"
## [1] 1349
## [1] "variable sizeb sample data:"
## [1] 0.05 0.05 0.05 0.05 0.05 0.05
## [1] "processing single col array"
## [1] "variable cldtop dim:"
## [1] 1349
## [1] "variable cldtop sample data:"
## [1] 1000 1000 1000 1000 1000 1000
## [1] "processing single col array"
## [1] "variable cod dim:"
## [1] 1349
## [1] "variable cod sample data:"
## [1] 1 1 1 1 1 1
## [1] "processing single col array"
## [1] "variable sza dim:"
## [1] 1349
## [1] "variable sza sample data:"
## [1] 10.00001 10.00001 10.00001 10.00001 10.00001 10.00001
## [1] "processing single col array"
## [1] "variable azi dim:"
## [1] 1349
## [1] "variable azi sample data:"
## [1] 0 2 5 10 20 30
## [1] "processing single col array"
## [1] "variable ref_i dim:"
## [1] 1349 7 640
## [1] "variable ref_i sample data:"
## [1] 0.2634877 0.2634730 0.2633957 0.2631150 0.2619549 0.2601073
## [1] "processing multiple col arrays"
## [1] "variable ref_q dim:"
## [1] 1349 7 640
## [1] "variable ref_q sample data:"
## [1] -0.1171747 -0.1171856 -0.1172425 -0.1174415 -0.1181891 -0.1193412
## [1] "processing multiple col arrays"
## [1] "processing computed variables"
## [1] "variable Rp dim:"
## [1] 1349 7 640
## [1] "variable Rp sample data:"
## [1] 0.1171747 0.1171856 0.1172425 0.1174415 0.1181891 0.1193412
## [1] "processing computed variables"
## [1] "variable DoLP dim:"
## [1] 1349 7 640
## [1] "variable DoLP sample data:"
## [1] 0.4447064 0.4447725 0.4451192 0.4463504 0.4511810 0.4588152
## [[1]]
## [1] 65536
Show some example curtain plots of simulated cloud LUT
subsetting reflectance (I) by lambda (n=7) and plotting curtains
## case sizea sizeb cldtop cod sza azi reflectance
## 1: 1 7.5 0.05 1000 1 10.00001 0 ref_i_lambda1_vza_1
## 2: 2 7.5 0.05 1000 1 10.00001 2 ref_i_lambda1_vza_1
## 3: 3 7.5 0.05 1000 1 10.00001 5 ref_i_lambda1_vza_1
## 4: 4 7.5 0.05 1000 1 10.00001 10 ref_i_lambda1_vza_1
## 5: 5 7.5 0.05 1000 1 10.00001 20 ref_i_lambda1_vza_1
## ---
## 6043516: 1345 20.0 0.05 2000 20 30.00000 0 ref_i_lambda7_vza_640
## 6043517: 1346 20.0 0.05 2000 20 30.00000 2 ref_i_lambda7_vza_640
## 6043518: 1347 20.0 0.05 2000 20 30.00000 5 ref_i_lambda7_vza_640
## 6043519: 1348 20.0 0.05 2000 20 30.00000 10 ref_i_lambda7_vza_640
## 6043520: 1349 20.0 0.05 2000 20 30.00000 20 ref_i_lambda7_vza_640
## value lambda
## 1: 0.2634877 lambda1
## 2: 0.2634730 lambda1
## 3: 0.2633957 lambda1
## 4: 0.2631150 lambda1
## 5: 0.2619549 lambda1
## ---
## 6043516: 0.3229581 lambda7
## 6043517: 0.3228281 lambda7
## 6043518: 0.3221557 lambda7
## 6043519: 0.3198731 lambda7
## 6043520: 0.3111509 lambda7
subsetting reflectance (I) by lambda (n=7) and COD
subsetting reflectance (I) by lambda (n=7) and Reff
subsetting reflectance (I) by lambda (n=7) and Azimuth angle
PCA summary
## [1] "summary of PCA for total (I) reflectance:"
## [1] "number of PC's that represent 0.99 variance:"
## PC1 PC2
## Standard deviation 11.47372 1.552867
## Proportion of Variance 0.96688 0.017710
## Cumulative Proportion 0.96688 0.984590
## [1] "most important PC's sdev:"
## [1] 11.473718 1.552867
## [1] "sample data rotation on PC space with VZA = 140"
## PC1 PC2
## ref_i_lambda1_vza_140 0.014782338 -0.002222145
## ref_i_lambda2_vza_140 0.016267666 -0.003531270
## ref_i_lambda3_vza_140 0.017596936 -0.004200948
## ref_i_lambda4_vza_140 0.018386640 -0.004091794
## ref_i_lambda5_vza_140 0.018926799 -0.002710358
## ref_i_lambda6_vza_140 0.014410177 0.015145155
## ref_i_lambda7_vza_140 0.009775086 0.027884634
PCA plots
## vars PC value lambda
## 1: ref_i_lambda1_vza_1 PC1 0.01017491 lambda1
## 2: ref_i_lambda1_vza_2 PC1 0.01023217 lambda1
## 3: ref_i_lambda1_vza_3 PC1 0.01028944 lambda1
## 4: ref_i_lambda1_vza_4 PC1 0.01034670 lambda1
## 5: ref_i_lambda1_vza_5 PC1 0.01040397 lambda1
## ---
## 8956: ref_i_lambda7_vza_636 PC2 0.03731711 lambda7
## 8957: ref_i_lambda7_vza_637 PC2 0.03741602 lambda7
## 8958: ref_i_lambda7_vza_638 PC2 0.03751493 lambda7
## 8959: ref_i_lambda7_vza_639 PC2 0.03761383 lambda7
## 8960: ref_i_lambda7_vza_640 PC2 0.03771274 lambda7
total reflectance by PC space
subsetting Rp by lambda (n=7) and plotting curtains
## case sizea sizeb cldtop cod sza azi reflectance
## 1: 1 7.5 0.05 1000 1 10.00001 0 Rp_lambda1_vza_1
## 2: 2 7.5 0.05 1000 1 10.00001 2 Rp_lambda1_vza_1
## 3: 3 7.5 0.05 1000 1 10.00001 5 Rp_lambda1_vza_1
## 4: 4 7.5 0.05 1000 1 10.00001 10 Rp_lambda1_vza_1
## 5: 5 7.5 0.05 1000 1 10.00001 20 Rp_lambda1_vza_1
## ---
## 6043516: 1345 20.0 0.05 2000 20 30.00000 0 Rp_lambda7_vza_640
## 6043517: 1346 20.0 0.05 2000 20 30.00000 2 Rp_lambda7_vza_640
## 6043518: 1347 20.0 0.05 2000 20 30.00000 5 Rp_lambda7_vza_640
## 6043519: 1348 20.0 0.05 2000 20 30.00000 10 Rp_lambda7_vza_640
## 6043520: 1349 20.0 0.05 2000 20 30.00000 20 Rp_lambda7_vza_640
## value lambda
## 1: 0.117174663 lambda1
## 2: 0.117185555 lambda1
## 3: 0.117242455 lambda1
## 4: 0.117441490 lambda1
## 5: 0.118189074 lambda1
## ---
## 6043516: 0.006922356 lambda7
## 6043517: 0.006889263 lambda7
## 6043518: 0.006720696 lambda7
## 6043519: 0.006188776 lambda7
## 6043520: 0.005069436 lambda7
PCA summary
## [1] "summary of PCA for Polarized reflectance (Rp):"
## [1] "number of PC's that represent 0.99 variance:"
## PC1 PC2 PC3 PC4 PC5
## Standard deviation 0.64070 0.4714032 0.3160951 0.2012885 0.156457
## Proportion of Variance 0.45502 0.2463200 0.1107500 0.0449100 0.027130
## Cumulative Proportion 0.45502 0.7013400 0.8120900 0.8570000 0.884140
## PC6 PC7 PC8 PC9 PC10
## Standard deviation 0.1437283 0.1303216 0.1117968 0.09312144 0.08738271
## Proportion of Variance 0.0229000 0.0188300 0.0138500 0.00961000 0.00846000
## Cumulative Proportion 0.9070300 0.9258600 0.9397100 0.94933000 0.95779000
## PC11 PC12 PC13 PC14
## Standard deviation 0.07989678 0.06828985 0.06281017 0.05958943
## Proportion of Variance 0.00708000 0.00517000 0.00437000 0.00394000
## Cumulative Proportion 0.96487000 0.97004000 0.97441000 0.97834000
## PC15 PC16 PC17 PC18
## Standard deviation 0.04917577 0.04546854 0.03906783 0.03731366
## Proportion of Variance 0.00268000 0.00229000 0.00169000 0.00154000
## Cumulative Proportion 0.98102000 0.98332000 0.98501000 0.98655000
## PC19 PC20
## Standard deviation 0.03626214 0.03202655
## Proportion of Variance 0.00146000 0.00114000
## Cumulative Proportion 0.98801000 0.98915000
## [1] "most important PC's sdev:"
## [1] 0.64070004 0.47140320 0.31609506 0.20128852 0.15645695 0.14372832
## [7] 0.13032158 0.11179679 0.09312144 0.08738271 0.07989678 0.06828985
## [13] 0.06281017 0.05958943 0.04917577 0.04546854 0.03906783 0.03731366
## [19] 0.03626214 0.03202655
## [1] "sample data rotation on PC space with VZA = 140"
## PC1 PC2 PC3 PC4
## Rp_lambda1_vza_140 -0.017522510 -0.003848304 0.0001060429 0.0051570234
## Rp_lambda2_vza_140 -0.014904247 -0.003438033 0.0003854994 0.0024755397
## Rp_lambda3_vza_140 -0.012441636 -0.003060451 0.0009232139 0.0010889801
## Rp_lambda4_vza_140 -0.010518289 -0.003151284 0.0010686383 0.0015478473
## Rp_lambda5_vza_140 -0.007859192 -0.002792449 0.0014015176 -0.0006187643
## Rp_lambda6_vza_140 -0.004481103 -0.003759145 0.0030529386 -0.0054049701
## Rp_lambda7_vza_140 -0.001950594 -0.001840152 0.0028868040 -0.0022480613
## PC5 PC6 PC7 PC8
## Rp_lambda1_vza_140 0.0001905565 -0.01104022 -0.0071842613 -0.0050054149
## Rp_lambda2_vza_140 0.0021657194 -0.01489962 -0.0046450996 -0.0034082476
## Rp_lambda3_vza_140 0.0014429995 -0.02093147 -0.0009913723 -0.0044392261
## Rp_lambda4_vza_140 0.0016938061 -0.02780078 0.0045958950 -0.0008796750
## Rp_lambda5_vza_140 -0.0036312889 -0.01925315 0.0058836988 -0.0007855336
## Rp_lambda6_vza_140 -0.0045341934 0.04320325 -0.0030760470 -0.0050404731
## Rp_lambda7_vza_140 -0.0061233724 0.03422672 0.0002391435 0.0012888644
## PC9 PC10 PC11 PC12
## Rp_lambda1_vza_140 -0.001965610 0.005604282 0.017490064 -0.012830940
## Rp_lambda2_vza_140 0.003068599 0.002397748 0.019745115 -0.016672522
## Rp_lambda3_vza_140 0.004400533 -0.001937114 0.019989845 -0.016122952
## Rp_lambda4_vza_140 0.003340147 -0.005634428 0.005219416 -0.018332741
## Rp_lambda5_vza_140 0.001543362 -0.009715388 -0.012810493 -0.005452900
## Rp_lambda6_vza_140 0.011088519 -0.006910806 0.004944261 0.004186598
## Rp_lambda7_vza_140 0.003312636 -0.016637229 0.004044170 0.004229350
## PC13 PC14 PC15 PC16
## Rp_lambda1_vza_140 0.017663835 -0.018407191 -0.003636992 0.006901258
## Rp_lambda2_vza_140 0.025786107 -0.019199705 -0.004309210 0.005527081
## Rp_lambda3_vza_140 0.019895083 -0.009989173 -0.002435173 0.001058991
## Rp_lambda4_vza_140 -0.009649026 0.011709646 -0.002878340 -0.004741615
## Rp_lambda5_vza_140 -0.066618391 0.041558707 0.010405370 -0.013090943
## Rp_lambda6_vza_140 -0.035545606 0.014540703 -0.001296554 0.001458236
## Rp_lambda7_vza_140 -0.023053114 0.010394593 0.015914739 0.005424229
## PC17 PC18 PC19 PC20
## Rp_lambda1_vza_140 -0.016899542 -0.0088332835 -0.0016678131 -0.0020800631
## Rp_lambda2_vza_140 -0.022149887 -0.0060527584 -0.0027920301 0.0009309976
## Rp_lambda3_vza_140 -0.026566701 -0.0065196215 -0.0070619475 0.0034960050
## Rp_lambda4_vza_140 -0.015558552 -0.0008640147 -0.0016248054 0.0047509235
## Rp_lambda5_vza_140 0.023387958 0.0069282575 0.0083433292 0.0044026760
## Rp_lambda6_vza_140 0.022043575 0.0032197887 0.0009026066 0.0030758608
## Rp_lambda7_vza_140 0.009522467 -0.0021835609 -0.0009938984 0.0088179412
PCA plots
## vars PC value lambda
## 1: Rp_lambda1_vza_1 PC1 -0.034823771 lambda1
## 2: Rp_lambda1_vza_2 PC1 -0.033388598 lambda1
## 3: Rp_lambda1_vza_3 PC1 -0.031953426 lambda1
## 4: Rp_lambda1_vza_4 PC1 -0.030518254 lambda1
## 5: Rp_lambda1_vza_5 PC1 -0.029083081 lambda1
## ---
## 89596: Rp_lambda7_vza_636 PC20 0.003467964 lambda7
## 89597: Rp_lambda7_vza_637 PC20 0.003430239 lambda7
## 89598: Rp_lambda7_vza_638 PC20 0.003376252 lambda7
## 89599: Rp_lambda7_vza_639 PC20 0.003318060 lambda7
## 89600: Rp_lambda7_vza_640 PC20 0.003256810 lambda7
polarized reflectance by PC space
subsetting DoLP by lambda (n=7) and plotting curtains
## case sizea sizeb cldtop cod sza azi reflectance
## 1: 1 7.5 0.05 1000 1 10.00001 0 DoLP_lambda1_vza_1
## 2: 2 7.5 0.05 1000 1 10.00001 2 DoLP_lambda1_vza_1
## 3: 3 7.5 0.05 1000 1 10.00001 5 DoLP_lambda1_vza_1
## 4: 4 7.5 0.05 1000 1 10.00001 10 DoLP_lambda1_vza_1
## 5: 5 7.5 0.05 1000 1 10.00001 20 DoLP_lambda1_vza_1
## ---
## 6043516: 1345 20.0 0.05 2000 20 30.00000 0 DoLP_lambda7_vza_640
## 6043517: 1346 20.0 0.05 2000 20 30.00000 2 DoLP_lambda7_vza_640
## 6043518: 1347 20.0 0.05 2000 20 30.00000 5 DoLP_lambda7_vza_640
## 6043519: 1348 20.0 0.05 2000 20 30.00000 10 DoLP_lambda7_vza_640
## 6043520: 1349 20.0 0.05 2000 20 30.00000 20 DoLP_lambda7_vza_640
## value lambda
## 1: 0.44470639 lambda1
## 2: 0.44477253 lambda1
## 3: 0.44511915 lambda1
## 4: 0.44635039 lambda1
## 5: 0.45118105 lambda1
## ---
## 6043516: 0.02143422 lambda7
## 6043517: 0.02134034 lambda7
## 6043518: 0.02086164 lambda7
## 6043519: 0.01934760 lambda7
## 6043520: 0.01629253 lambda7
subsetting DoLP by lambda (n=7) and COD
subsetting DoLP by lambda (n=7) and Reff
subsetting DoLP by lambda (n=7) and Azimuth angle
PCA summary
## [1] "summary of PCA for DoLP:"
## [1] "number of PC's that represent 0.99 variance:"
## PC1 PC2 PC3 PC4 PC5
## Standard deviation 5.340889 2.656646 1.586771 0.8866456 0.6704982
## Proportion of Variance 0.686100 0.169760 0.060560 0.0189100 0.0108100
## Cumulative Proportion 0.686100 0.855850 0.916410 0.9353200 0.9461300
## PC6 PC7 PC8 PC9 PC10
## Standard deviation 0.6461746 0.5642162 0.527823 0.4598133 0.3972724
## Proportion of Variance 0.0100400 0.0076600 0.006700 0.0050900 0.0038000
## Cumulative Proportion 0.9561800 0.9638300 0.970530 0.9756200 0.9794200
## PC11 PC12 PC13 PC14 PC15
## Standard deviation 0.3246901 0.3187232 0.3068874 0.2645914 0.2443863
## Proportion of Variance 0.0025400 0.0024400 0.0022700 0.0016800 0.0014400
## Cumulative Proportion 0.9819500 0.9843900 0.9866600 0.9883400 0.9897800
## [1] "most important PC's sdev:"
## [1] 5.3408887 2.6566461 1.5867708 0.8866456 0.6704982 0.6461746 0.5642162
## [8] 0.5278230 0.4598133 0.3972724 0.3246901 0.3187232 0.3068874 0.2645914
## [15] 0.2443863
## [1] "sample data rotation on PC space with VZA = 140"
## PC1 PC2 PC3 PC4
## DoLP_lambda1_vza_140 -0.003278391 -0.013338933 -0.002689673 -0.0036474037
## DoLP_lambda2_vza_140 -0.003805271 -0.013872688 -0.002771832 -0.0029547146
## DoLP_lambda3_vza_140 -0.004102361 -0.014394168 -0.002835032 -0.0012778368
## DoLP_lambda4_vza_140 -0.004198328 -0.013816511 -0.003699108 0.0013053574
## DoLP_lambda5_vza_140 -0.004257772 -0.010637554 -0.004329285 -0.0007822416
## DoLP_lambda6_vza_140 -0.004648121 -0.007144787 -0.006788056 -0.0153028500
## DoLP_lambda7_vza_140 -0.004171260 -0.003625122 -0.002922232 -0.0107596570
## PC5 PC6 PC7 PC8
## DoLP_lambda1_vza_140 0.004724829 -0.001993265 -0.004129317 -0.010203199
## DoLP_lambda2_vza_140 0.007623034 -0.005222798 -0.007104072 -0.009568091
## DoLP_lambda3_vza_140 0.014543207 -0.011193667 -0.008765989 -0.009175001
## DoLP_lambda4_vza_140 0.024836271 -0.017970328 -0.004800820 -0.012873435
## DoLP_lambda5_vza_140 0.015848280 -0.018350437 0.004947381 -0.007885042
## DoLP_lambda6_vza_140 -0.040158830 0.021127306 0.009322353 0.028394572
## DoLP_lambda7_vza_140 -0.030929761 0.020026069 0.010689546 0.024690201
## PC9 PC10 PC11 PC12
## DoLP_lambda1_vza_140 0.0060424368 0.0042911509 0.010875612 -0.002879173
## DoLP_lambda2_vza_140 0.0020117678 0.0003630089 0.014921095 -0.007225222
## DoLP_lambda3_vza_140 -0.0042791882 0.0002508327 0.015201546 -0.005524545
## DoLP_lambda4_vza_140 -0.0104992897 -0.0033687299 -0.015193177 0.001846259
## DoLP_lambda5_vza_140 -0.0127217540 0.0071331781 -0.057166649 0.027480302
## DoLP_lambda6_vza_140 -0.0029847967 0.0078305491 -0.008313100 0.014349606
## DoLP_lambda7_vza_140 0.0000946789 0.0034020636 -0.003559903 0.027669107
## PC13 PC14 PC15
## DoLP_lambda1_vza_140 0.007053612 -0.012669736 0.007648119
## DoLP_lambda2_vza_140 0.015229216 -0.017362430 0.007107384
## DoLP_lambda3_vza_140 0.016669194 -0.021483545 0.002182318
## DoLP_lambda4_vza_140 -0.007445787 -0.017958109 -0.007128668
## DoLP_lambda5_vza_140 -0.070012775 0.003254592 -0.014918609
## DoLP_lambda6_vza_140 -0.047009933 -0.013162646 -0.005461758
## DoLP_lambda7_vza_140 -0.021942509 -0.009989280 -0.001053359
PCA plots
## vars PC value lambda
## 1: DoLP_lambda1_vza_1 PC1 -0.011439571 lambda1
## 2: DoLP_lambda1_vza_2 PC1 -0.011431089 lambda1
## 3: DoLP_lambda1_vza_3 PC1 -0.011421716 lambda1
## 4: DoLP_lambda1_vza_4 PC1 -0.011411446 lambda1
## 5: DoLP_lambda1_vza_5 PC1 -0.011400275 lambda1
## ---
## 67196: DoLP_lambda7_vza_636 PC15 -0.004144798 lambda7
## 67197: DoLP_lambda7_vza_637 PC15 -0.004139530 lambda7
## 67198: DoLP_lambda7_vza_638 PC15 -0.004098064 lambda7
## 67199: DoLP_lambda7_vza_639 PC15 -0.004053079 lambda7
## 67200: DoLP_lambda7_vza_640 PC15 -0.004006749 lambda7
DoLP by PC space